Mock Version: 1.2.12
ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec'], chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-3154/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=<mockbuild.trace_decorator.getLog object at 0x7fa4cb81fed0>uid=1001)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target x86_64 --nodeps /builddir/build/SPECS/bowtie.spec'] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
warning: Could not canonicalize hostname: copr-builder-442482528.novalocal
Building target platforms: x86_64
Building for target x86_64
Wrote: /builddir/build/SRPMS/bowtie-1.1.2-1.el7.centos.src.rpm
Child return code was: 0
LEAVE do --> 

ENTER do(['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps  /builddir/build/SPECS/bowtie.spec '], chrootPath='/var/lib/mock/epel-7-x86_64-mockbuilder-3154/root'shell=FalseprintOutput=Falseenv={'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'}gid=135user='mockbuild'timeout=0logger=<mockbuild.trace_decorator.getLog object at 0x7fa4cb81fed0>uid=1001)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target x86_64 --nodeps  /builddir/build/SPECS/bowtie.spec '] with env {'LANG': 'en_US.UTF-8', 'TERM': 'vt100', 'SHELL': '/bin/bash', 'PROMPT_COMMAND': 'printf "\x1b]0;<mock-chroot>\x07<mock-chroot>"', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'HOME': '/builddir', 'HOSTNAME': 'mock'} and shell False
Building target platforms: x86_64
Building for target x86_64
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.E02yGe
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf bowtie-1.1.2
+ /usr/bin/unzip -qq /builddir/build/SOURCES/bowtie-1.1.2-src.zip
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd bowtie-1.1.2
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.aoE53t
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie-1.1.2
+ make -j2 'EXTRA_CFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic' 'EXTRA_CXXFLAGS=-O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic' BAM_LDFLAGS=
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
	-I SeqAn-1.1 -I third_party -I third_party \
	-o bowtie-build-s ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
	-lpthread 
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic  \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -DNDEBUG -Wall \
	-I SeqAn-1.1 -I third_party -I third_party \
	-o bowtie-build-l ebwt_build.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp  bowtie_build_main.cpp \
	-lpthread 
/bin/sh: hostname: command not found
/bin/sh: hostname: command not found
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from ebwt_build.cpp:7:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:27:0,
                 from ebwt_build.cpp:11:
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:40:0,
                 from ebwt_build.cpp:11:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
    uint64_t origBufOff = bufOff;
             ^
reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
          bool binarySearched = false;
               ^
In file included from ebwt.h:40:0,
                 from ebwt_build.cpp:11:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
    uint64_t origBufOff = bufOff;
             ^
reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
          bool binarySearched = false;
               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:102:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:46:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                                     ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/index.h:27,
                 from ebwt_build.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:102:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:46:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                                     ^
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:731:88:   required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
ebwt.h:4032:32:   required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = unsigned int; uint32_t = unsigned int]'
ebwt_build.cpp:485:9:   required from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]'
ebwt_build.cpp:622:69:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:731:88:   required from 'typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Alloc<void>; _TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
ebwt.h:4032:32:   required from 'static TStr Ebwt<TStr>::join(std::vector<FileBuf*>&, std::vector<RefRecord>&, TIndexOffU, const RefReadInParams&, uint32_t) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = long unsigned int; uint32_t = unsigned int]'
ebwt_build.cpp:485:9:   required from 'void driver(const string&, std::vector<std::basic_string<char> >&, const string&, bool) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::string = std::basic_string<char>]'
ebwt_build.cpp:622:69:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -Wall \
	-I SeqAn-1.1 -I third_party -I third_party \
	-o bowtie-align-s ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	-lpthread 
/bin/sh: hostname: command not found
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DNDEBUG -DBOWTIE_64BIT_INDEX -Wall \
	-I SeqAn-1.1 -I third_party -I third_party \
	-o bowtie-align-l ebwt_search.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp refmap.cpp annot.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \
	-lpthread 
/bin/sh: hostname: command not found
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/find.h:62:0,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
  typedef unsigned int TWord;
                       ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ebwt_search.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ebwt_search.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt.h:16,
                 from ebwt_search.cpp:14:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt.h:16,
                 from ebwt_search.cpp:14:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/find.h:62:0,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
  typedef unsigned int TWord;
                       ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ebwt_search.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ebwt_search.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from ebwt.h:27:0,
                 from ebwt_search.cpp:14:
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt.h:16,
                 from ebwt_search.cpp:14:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt.h:16,
                 from ebwt_search.cpp:14:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
In file included from ebwt.h:27:0,
                 from ebwt_search.cpp:14:
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:40:0,
                 from ebwt_search.cpp:14:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
    uint64_t origBufOff = bufOff;
             ^
reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
          bool binarySearched = false;
               ^
In file included from ebwt.h:27:0,
                 from ebwt_search.cpp:14:
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:27:0,
                 from ebwt_search.cpp:14:
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:40:0,
                 from ebwt_search.cpp:14:
reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const':
reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable]
    uint64_t origBufOff = bufOff;
             ^
reference.h:528:15: warning: variable 'binarySearched' set but not used [-Wunused-but-set-variable]
          bool binarySearched = false;
               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:102:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:46:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                                     ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from ebwt_search.cpp:8:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:102:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:46:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from pat.cpp:5:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from pat.cpp:6:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from pat.cpp:6:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from pat.cpp:5:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from pat.cpp:5:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from pat.cpp:6:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from pat.cpp:6:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from ebwt_search_util.h:9,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from ebwt_search_util.h:9,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ebwt_search_util.h:8,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from ebwt_search_util.h:9,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from ebwt_search_util.h:9,
                 from ebwt_search_util.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit_set.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit_set.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from hit_set.cpp:10:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit_set.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit_set.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from pat.h:13,
                 from sam.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from pat.h:13,
                 from sam.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from pat.h:12,
                 from sam.cpp:11:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from pat.h:13,
                 from sam.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from pat.h:13,
                 from sam.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from alphabet.h:6,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from color_dec.cpp:11:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from hit.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from hit.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from hit.h:11,
                 from hit.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from hit.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from hit.h:12,
                 from hit.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
g++ -O3 -m64 \
	-DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -Wall \
	-I SeqAn-1.1 -I third_party -I third_party -I . \
	-o bowtie-inspect-s bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
	-lpthread
/bin/sh: hostname: command not found
g++ -O3 -m64 \
	-DCOMPILER_OPTIONS="\"-O3 -m64  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic\""  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches   -m64 -mtune=generic \
	-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE  -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -DBOWTIE_64BIT_INDEX -Wall \
	-I SeqAn-1.1 -I third_party -I third_party -I . \
	-o bowtie-inspect-l bowtie_inspect.cpp \
	ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp \
	-lpthread
/bin/sh: hostname: command not found
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/find.h:62:0,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
  typedef unsigned int TWord;
                       ^
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt.h:16,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt.h:16,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ebwt.h:24,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ebwt.h:24,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/find.h:62:0,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/find/find_multiple_shiftand.h: In function 'void seqan::_patternInit(seqan::Pattern<TNeedle, seqan::Tag<seqan::_MultipleShiftAnd> >&)':
SeqAn-1.1/seqan/find/find_multiple_shiftand.h:220:23: warning: typedef 'TWord' locally defined but not used [-Wunused-local-typedefs]
  typedef unsigned int TWord;
                       ^
In file included from SeqAn-1.1/seqan/index.h:82:0,
                 from ebwt.h:16,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<0u> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<0u> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:273:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, SimpleShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedShape<q> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedShape<q> >&, TIter)':
SeqAn-1.1/seqan/index/shape_base.h:309:65: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedShape<q> > >::Type THValue;
                                                                 ^
SeqAn-1.1/seqan/index/shape_base.h:310:64: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Size< Shape<TValue, FixedShape<q> > >::Type TSize;
                                                                ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:322:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hashUpper(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:424:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
SeqAn-1.1/seqan/index/shape_base.h: In function 'typename seqan::Value<seqan::Shape<TValue, TSpec> >::Type seqan::hash2(seqan::Shape<TValue, TSpec>&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_base.h:492:56: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, TSpec> >::Type THValue;
                                                        ^
In file included from SeqAn-1.1/seqan/index.h:83:0,
                 from ebwt.h:16,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<const seqan::Tag<seqan::Default_> > >&, TIter)':
SeqAn-1.1/seqan/index/shape_gapped.h:370:62: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, GappedShape> >::Type THValue;
                                                              ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hash(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:387:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
SeqAn-1.1/seqan/index/shape_gapped.h: In function 'typename seqan::Value<seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> > >::Type seqan::hashUpper(seqan::Shape<TValue, seqan::FixedGappedShape<TSpec> >&, TIter, TSize)':
SeqAn-1.1/seqan/index/shape_gapped.h:415:75: warning: typedef 'THValue' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Value< Shape<TValue, FixedGappedShape<TSpec> > >::Type THValue;
                                                                           ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ebwt.h:24,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ebwt.h:24,
                 from bowtie_inspect.cpp:10:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from ebwt.h:27:0,
                 from bowtie_inspect.cpp:10:
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:27:0,
                 from bowtie_inspect.cpp:10:
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:27:0,
                 from bowtie_inspect.cpp:10:
blockwise_sa.h: In member function 'void KarkkainenBlockwiseSA<TStr>::buildSamples()':
blockwise_sa.h:380:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from ebwt.h:27:0,
                 from bowtie_inspect.cpp:10:
blockwise_sa.h: In member function 'virtual void KarkkainenBlockwiseSA<TStr>::nextBlock()':
blockwise_sa.h:755:37: warning: typedef 'TAlphabet' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TStr>::Type TAlphabet;
                                     ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:102:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:46:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                                     ^
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:509:6:   required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_base.h:1429:52:   required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_base.h:1459:67:   required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]'
ebwt.h:2965:35:   required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
bowtie_inspect.cpp:283:2:   required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]'
bowtie_inspect.cpp:461:42:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from SeqAn-1.1/seqan/find.h:31,
                 from bowtie_inspect.cpp:6:
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:906:102:   required from 'typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::position(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Position<const seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_packed.h:1237:40:   required from 'typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type seqan::operator-(const seqan::Iter<TContainer, seqan::Packed<THostspec> >&, const seqan::Iter<TContainer, seqan::Packed<THostspec> >&) [with TContainer = const seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; THostspec = seqan::Alloc<void>; typename seqan::Difference<seqan::Iter<TContainer, seqan::Packed<THostspec> > >::Type = long int]'
SeqAn-1.1/seqan/sequence/string_base.h:181:29:   required from 'typename seqan::Size<const seqan::String<TValue, TSpec> >::Type seqan::length(const seqan::String<TValue, TSpec>&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; typename seqan::Size<const seqan::String<TValue, TSpec> >::Type = long unsigned int]'
blockwise_sa.h:354:46:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
   VALUES_PER_WORD = (BITS_PER_VALUE > BITS_PER_HOST_VALUE) ? 1 : (BITS_PER_HOST_VALUE / BITS_PER_VALUE),
                                     ^
SeqAn-1.1/seqan/sequence/string_packed.h: In instantiation of 'struct seqan::_PackedConsts<seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> > >':
SeqAn-1.1/seqan/sequence/string_packed.h:509:6:   required from 'typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type seqan::capacity(const seqan::String<TValue, seqan::Packed<THostspec> >&) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; THostspec = seqan::Alloc<void>; typename seqan::Size<const seqan::String<TValue, seqan::Packed<THostspec> > >::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_base.h:1429:52:   required from 'static typename seqan::Size<T>::Type seqan::_Resize_String<TExpand>::resize_(T&, typename seqan::Size<T>::Type) [with T = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TExpand = const seqan::Tag<seqan::TagExact_>; typename seqan::Size<T>::Type = long unsigned int]'
SeqAn-1.1/seqan/sequence/string_base.h:1459:67:   required from 'typename seqan::Size<seqan::String<TValue, TSpec> >::Type seqan::resize(seqan::String<TValue, TSpec>&, TSize, seqan::Tag<TUsage>) [with TValue = seqan::SimpleType<unsigned char, seqan::_Dna>; TSpec = seqan::Packed<>; TSize = long unsigned int; TExpand = seqan::TagExact_; typename seqan::Size<seqan::String<TValue, TSpec> >::Type = long unsigned int]'
ebwt.h:2965:35:   required from 'void Ebwt<TStr>::restore(TStr&) const [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >]'
bowtie_inspect.cpp:283:2:   required from 'void print_index_sequences(std::ostream&, Ebwt<TStr>&, const BitPairReference&) [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; std::ostream = std::basic_ostream<char>]'
bowtie_inspect.cpp:461:42:   required from here
SeqAn-1.1/seqan/sequence/string_packed.h:294:37: warning: comparison between 'enum seqan::BitsPerValue<seqan::SimpleType<unsigned char, seqan::_Dna> >::<anonymous>' and 'enum seqan::BitsPerValue<unsigned int>::<anonymous>' [-Wenum-compare]
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
In file included from SeqAn-1.1/seqan/basic.h:64:0,
                 from SeqAn-1.1/seqan/sequence.h:27,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::setValue(seqan::Holder<TValue, seqan::Tristate2>&, TValue&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1001:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'typename seqan::Reference<seqan::Holder<TValue, seqan::Tristate2> >::Type seqan::value(seqan::Holder<TValue, seqan::Tristate2>&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1027:59: warning: typedef 'THolderType' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THolderType;
                                                           ^
SeqAn-1.1/seqan/basic/basic_holder.h: In function 'void seqan::assignValue(seqan::Holder<TValue, seqan::Tristate2>&, const TSource&)':
SeqAn-1.1/seqan/basic/basic_holder.h:1051:59: warning: typedef 'THostValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<Holder<TValue, Tristate2> >::Type THostValue;
                                                           ^
In file included from SeqAn-1.1/seqan/sequence.h:38:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/lexical.h: In function 'void seqan::compare_(seqan::Lexical<TSpec>&, TLeft&, TRight&)':
SeqAn-1.1/seqan/sequence/lexical.h:239:38: warning: typedef 'TLeftValue' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Value<TLeft>::Type TLeftValue;
                                      ^
In file included from SeqAn-1.1/seqan/sequence.h:51:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:811:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSource&, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:821:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:834:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::assign(seqan::String<TValue, TSpec>&, const TSourceValue*, TSize, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:844:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1044:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1056:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1070:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::append(seqan::String<TValue, TSpec>&, TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1082:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1249:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSource&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1263:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1279:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
SeqAn-1.1/seqan/sequence/string_base.h: In function 'void seqan::replace(seqan::String<TValue, TSpec>&, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, const TSourceValue*, typename seqan::Size<seqan::String<TValue, TSpec> >::Type, seqan::Tag<TUsage>)':
SeqAn-1.1/seqan/sequence/string_base.h:1293:44: warning: typedef 'TTarget' locally defined but not used [-Wunused-local-typedefs]
  typedef String<TTargetValue, TTargetSpec> TTarget;
                                            ^
In file included from SeqAn-1.1/seqan/sequence.h:53:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_alloc.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Alloc<TSpec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_alloc.h:456:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:57:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/string_packed.h: In static member function 'static typename seqan::Size<T>::Type seqan::_ClearSpace_String_Packed_<TExpand>::_clearSpace_(T&, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type, typename seqan::Size<T>::Type)':
SeqAn-1.1/seqan/sequence/string_packed.h:594:48: warning: typedef 'TIterator' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Iterator<T, Standard>::Type TIterator;
                                                ^
SeqAn-1.1/seqan/sequence/string_packed.h: In function 'typename seqan::Size<seqan::String<TValue, seqan::Alloc<TSpec> > >::Type seqan::reserve(seqan::String<TValue, seqan::Packed<THostspec> >&, _TSize, Insist)':
SeqAn-1.1/seqan/sequence/string_packed.h:758:63: warning: typedef 'TSize' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Size< String<TValue, Alloc<TSpec> > >::Type TSize;
                                                               ^
In file included from SeqAn-1.1/seqan/sequence.h:62:0,
                 from ref_read.h:11,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/sequence/sequence_multiple.h: In function 'void seqan::subset(seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, seqan::StringSet<TString, seqan::Dependent<const seqan::Tag<seqan::TagGenerous_> > >&, TIds, TLength)':
SeqAn-1.1/seqan/sequence/sequence_multiple.h:1647:41: warning: typedef 'TId' locally defined but not used [-Wunused-local-typedefs]
   typedef typename Id<TStringSet>::Type TId;
                                         ^
In file included from SeqAn-1.1/seqan/file.h:66:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::read(TFile&, seqan::Align<TSource, TSpec>&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:138:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
SeqAn-1.1/seqan/file/file_format_fasta_align.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, FastaAlign)':
SeqAn-1.1/seqan/file/file_format_fasta_align.h:252:42: warning: typedef 'TPosition' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Position<TAlign>::Type TPosition;
                                          ^
In file included from SeqAn-1.1/seqan/file.h:69:0,
                 from alphabet.h:7,
                 from ref_read.h:12,
                 from ref_read.cpp:1:
SeqAn-1.1/seqan/file/file_format_cgviz.h: In function 'void seqan::_write_impl(TFile&, seqan::Align<TSource, TSpec>&, TStringContainer&, CGViz)':
SeqAn-1.1/seqan/file/file_format_cgviz.h:66:37: warning: typedef 'TRow' locally defined but not used [-Wunused-local-typedefs]
  typedef typename Row<TAlign>::Type TRow;
                                     ^
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.8A0MmR
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64
++ dirname /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64
+ cd bowtie-1.1.2
+ rm -rf /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64
+ mkdir -p /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/bin
+ mkdir -p /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/share/bowtie
+ install -m 0755 bowtie /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/bin
+ install -m 0755 bowtie-build /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/bin
+ install -m 0755 bowtie-inspect /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/bin
+ cp -a reads /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/share/bowtie/
+ cp -a indexes /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/share/bowtie/
+ cp -a genomes /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/share/bowtie/
+ cp -a scripts /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64//usr/share/bowtie/
+ /usr/lib/rpm/find-debuginfo.sh --strict-build-id -m --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 /builddir/build/BUILD/bowtie-1.1.2
/usr/lib/rpm/sepdebugcrcfix: Updated 0 CRC32s, 0 CRC32s did match.
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-java-repack-jars
Processing files: bowtie-1.1.2-1.el7.centos.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.GbR7Te
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie-1.1.2
+ DOCDIR=/builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ cp -pr MANUAL /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ cp -pr NEWS /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ cp -pr VERSION /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ cp -pr AUTHORS /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ cp -pr TUTORIAL /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ cp -pr doc/manual.html doc/style.css /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/doc/bowtie-1.1.2
+ exit 0
Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.aXONtC
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie-1.1.2
+ LICENSEDIR=/builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/licenses/bowtie-1.1.2
+ export LICENSEDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/licenses/bowtie-1.1.2
+ cp -pr SeqAn-1.1/GPL.txt SeqAn-1.1/LGPL.txt /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64/usr/share/licenses/bowtie-1.1.2
+ exit 0
Provides: bowtie = 1.1.2-1.el7.centos bowtie(x86-64) = 1.1.2-1.el7.centos
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/sh /usr/bin/env /usr/bin/perl perl(Getopt::Long) perl(List::Util) perl(strict) perl(warnings)
Processing files: bowtie-debuginfo-1.1.2-1.el7.centos.x86_64
Provides: bowtie-debuginfo = 1.1.2-1.el7.centos bowtie-debuginfo(x86-64) = 1.1.2-1.el7.centos
Requires(rpmlib): rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 rpmlib(CompressedFileNames) <= 3.0.4-1
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64
warning: Could not canonicalize hostname: copr-builder-442482528.novalocal
Wrote: /builddir/build/RPMS/bowtie-1.1.2-1.el7.centos.x86_64.rpm
Wrote: /builddir/build/RPMS/bowtie-debuginfo-1.1.2-1.el7.centos.x86_64.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.2aldca
+ umask 022
+ cd /builddir/build/BUILD
+ cd bowtie-1.1.2
+ rm -rf /builddir/build/BUILDROOT/bowtie-1.1.2-1.el7.centos.x86_64
+ exit 0
Child return code was: 0
LEAVE do -->